This is almost more stupid than the "Mario is wearing animal skins" thing. Every single Pokemon game has addressed the capturing thing and the morality of training Pokemon was even the main plot in Black and White.

All this achieves is making PETA sound exactly like Team Plasma.. you know, the bad guys?

Indeed, it'd have made a lot more sense if Black & White hadn't addressed most of the issues that brought up as part of its main plot. Plus it's a universe where you can regenerate a creature (who was already fighting willingly, as per the story of the game) to peak condition with a simple machine that's free to use.

The mission statement for that mini-game definitely has PETA as the bad guys. Fairly misguided really, as are all their minigames.